Abhisit's former deputy, Suthep Thaugsuban, was also charged with premeditated murder, the Bangkok Post reported.
A court recently determined the victim, Phan Khamkong, was shot during a street demonstration by soldiers acting under orders from the Center for the Resolution of the Emergency Situation, headed by Suthep.
The soldiers involved will not face charges, the newspaper said.
About 50 people were killed in violent protests that erupted in Bangkok in 2010. Many of the protesters were supporters of Thaksin Shinawatra, a former protester ousted by a coup in 2007.
The killing of Phan is the first to get to the point of criminal charges, The New York Times reported, but is unlikely to be the last.
Tharit Pengdit, director of the Department of Special Investigation, said orders from Abhisit and Suthep "caused the deaths of many people."
Thaksin's sister, Yingluck Shinawatra, is now prime minister. Her brother remains in exile.